But you've indicated the issue. The Dualshock 3 didn't easily charge via USB, as it didn't charge via a standard wall charger. It required a data connection so it would only charge when the PS3 was switched on or from a computer.

The USB standards to charge without requiring a data connection were brought in a couple of years earlier but weren't really common yet

I don't feel like that really undercuts what I said though. USB charging was quite uncommon in 2006 when the PS3 came out, which is why it was defensible for the 2004-5 DS to have avoided it. It was quite common by 2011 though, which is why I don't think it was still defensible for the 3DS to have avoided it.